A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
- Pipeline version
- v1.0.0
- Contact E-mail
- qtl7@cdc.gov
- Project Type
- HMAS tripod analysis
Report generated on 2024-09-07, 00:04 EDT based on data in:
/scicomp/groups-pure/OID/NCEZID/DFWED/EDLB/projects/CIMS/HMAS_pilot/tripod/dev/multiqc_config.yaml/scicomp/groups-pure/OID/NCEZID/DFWED/EDLB/projects/CIMS/HMAS_pilot/tripod/dev/work/87/26b7282c434172c72533d9e84e9123
quast_report
Assembly Statistics using Quast.
| Sample Name | N50 (Kbp) | # of contigs >= 1Kbp | Largest contig (Kbp) | Length (Kbp) |
|---|---|---|---|---|
| CIMS-MN-055-SH-K-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-055-SH-M-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-055-IW-M-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-053-SH-K-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-053-IW-K-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-068-IW-M-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-068-SH-M-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-069-SH-M-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-069-IW-M-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-050-SH-K-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-067-SH-K-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-058-SH-K-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-065-IW-K-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-050-SH-M-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-056-IW-M-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-056-IW-K-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-050-IW-K-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-064-SH-M-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-065-SH-K-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-065-SH-M-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-064-SH-K-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-049-IW-K-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-070-IW-M-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-070-SH-M-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-062-SH-K-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-057-IW-M-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-057-IW-K-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-057-SH-M-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-061-IW-M-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-059-IW-K-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-059-IW-M-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-059-SH-K-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-051-IW-M-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-051-SH-M-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-050-IW-M-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-051-SH-K-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-055-IW-K-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-069-IW-K-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-058-IW-K-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-069-SH-K-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-067-IW-K-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-065-IW-M-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-056-SH-K-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-062-SH-M-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-049-SH-K-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-056-SH-M-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-064-IW-K-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-063-IW-M-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-067-SH-M-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-063-SH-K-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-049-IW-M-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-054-SH-K-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
| CIMS-MN-053-SH-M-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-054-IW-M-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
| CIMS-MN-058-IW-M-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-060-IW-K-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-061-SH-K-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-061-SH-M-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-059-SH-M-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-068-SH-K-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-063-SH-M-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-060-SH-K-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-053-IW-M-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-049-SH-M-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-058-SH-M-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-054-IW-K-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
| CIMS-MN-051-IW-K-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-061-IW-K-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-067-IW-M-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-068-IW-K-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-062-IW-M-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-064-IW-M-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-062-IW-K-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-070-IW-K-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-070-SH-K-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-063-IW-K-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-060-IW-M-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-060-SH-M-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-057-SH-K-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-054-SH-M-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
tripod report
Combined summary statistics for all the samples in the run, primer pairs (out of total 2461 in the Salmonella HMAS primer panel).
| Sample Name | # of FP | # of not ident seqs | # of matched most abund. seqs | % of matched most abund. seqs |
|---|---|---|---|---|
| CIMS-MN-108-MN-M05688-240618_S47 | 2 | 0 | 0 / 2 | 0.000 |
| CIMS-MN-106-MN-M05688-240618_S23 | 3 | 0 | 0 / 3 | 0.000 |
| CIMS-MN-105-MN-M05688-240618_S4 | 8 | 0 | 0 / 8 | 0.000 |
| CIMS-MN-080-IH-MN-M05688-240618_S26 | 2443 | 0 | 0 / 2443 | 0.000 |
| CIMS-MN-063-IH-MN-M05688-240618_S15 | 112 | 17 | 2320 / 2449 | 0.947 |
| CIMS-MN-099-IH-MN-M05688-240618_S45 | 2448 | 0 | 0 / 2448 | 0.000 |
| CIMS-MN-069-IH-MN-M05688-240618_S21 | 119 | 34 | 2296 / 2449 | 0.938 |
| CIMS-MN-058-IH-MN-M05688-240618_S10 | 143 | 28 | 2278 / 2449 | 0.930 |
| CIMS-MN-086-IH-MN-M05688-240618_S32 | 2439 | 0 | 0 / 2439 | 0.000 |
| CIMS-MN-091-IH-MN-M05688-240618_S37 | 2448 | 0 | 0 / 2448 | 0.000 |
| CIMS-MN-093-IH-MN-M05688-240618_S39 | 2443 | 0 | 0 / 2443 | 0.000 |
| CIMS-MN-083-IH-MN-M05688-240618_S29 | 2447 | 0 | 0 / 2447 | 0.000 |
| CIMS-MN-082-IH-MN-M05688-240618_S28 | 2447 | 0 | 0 / 2447 | 0.000 |
| CIMS-MN-060-IH-MN-M05688-240618_S12 | 112 | 16 | 2322 / 2450 | 0.948 |
| CIMS-MN-068-IH-MN-M05688-240618_S20 | 117 | 20 | 2311 / 2448 | 0.944 |
| CIMS-MN-057-IH-MN-M05688-240618_S9 | 112 | 17 | 2320 / 2449 | 0.947 |
| CIMS-MN-054-IH-MN-M05688-240618_S6 | 116 | 36 | 2296 / 2448 | 0.938 |
| CIMS-MN-066-IH-MN-M05688-240618_S18 | 2450 | 0 | 0 / 2450 | 0.000 |
| CIMS-MN-088-IH-MN-M05688-240618_S34 | 2448 | 0 | 0 / 2448 | 0.000 |
| CIMS-MN-090-IH-MN-M05688-240618_S36 | 2440 | 0 | 0 / 2440 | 0.000 |
| CIMS-MN-050-IH-MN-M05688-240618_S2 | 134 | 31 | 2279 / 2444 | 0.932 |
| CIMS-MN-092-IH-MN-M05688-240618_S38 | 2447 | 0 | 0 / 2447 | 0.000 |
| CIMS-MN-067-IH-MN-M05688-240618_S19 | 112 | 14 | 2322 / 2448 | 0.949 |
| CIMS-MN-085-IH-MN-M05688-240618_S31 | 2449 | 0 | 0 / 2449 | 0.000 |
| CIMS-MN-061-IH-MN-M05688-240618_S13 | 112 | 18 | 2323 / 2453 | 0.947 |
| CIMS-MN-087-IH-MN-M05688-240618_S33 | 2449 | 0 | 0 / 2449 | 0.000 |
| CIMS-MN-089-IH-MN-M05688-240618_S35 | 2452 | 0 | 0 / 2452 | 0.000 |
| CIMS-MN-056-IH-MN-M05688-240618_S8 | 117 | 26 | 2308 / 2451 | 0.942 |
| CIMS-MN-079-IH-MN-M05688-240618_S25 | 2452 | 0 | 0 / 2452 | 0.000 |
| CIMS-MN-095-IH-MN-M05688-240618_S41 | 2449 | 0 | 0 / 2449 | 0.000 |
| CIMS-MN-096-IH-MN-M05688-240618_S42 | 2451 | 0 | 0 / 2451 | 0.000 |
| CIMS-MN-097-IH-MN-M05688-240618_S43 | 2447 | 0 | 0 / 2447 | 0.000 |
| CIMS-MN-062-IH-MN-M05688-240618_S14 | 113 | 16 | 2322 / 2451 | 0.947 |
| CIMS-MN-098-IH-MN-M05688-240618_S44 | 2451 | 0 | 0 / 2451 | 0.000 |
| CIMS-MN-081-IH-MN-M05688-240618_S27 | 2450 | 0 | 0 / 2450 | 0.000 |
| CIMS-MN-053-IH-MN-M05688-240618_S5 | 113 | 20 | 2318 / 2451 | 0.946 |
| CIMS-MN-064-IH-MN-M05688-240618_S16 | 113 | 17 | 2322 / 2452 | 0.947 |
| CIMS-MN-051-IH-MN-M05688-240618_S3 | 119 | 15 | 2318 / 2452 | 0.945 |
| CIMS-MN-059-IH-MN-M05688-240618_S11 | 112 | 16 | 2323 / 2451 | 0.948 |
| CIMS-MN-065-IH-MN-M05688-240618_S17 | 113 | 15 | 2324 / 2452 | 0.948 |
| CIMS-MN-049-IH-MN-M05688-240618_S1 | 113 | 18 | 2318 / 2449 | 0.947 |
| CIMS-MN-109-IH-MN-M05688-240618_S48 | 2452 | 0 | 0 / 2452 | 0.000 |
| CIMS-MN-055-IH-MN-M05688-240618_S7 | 113 | 17 | 2323 / 2453 | 0.947 |
| CIMS-MN-094-IH-MN-M05688-240618_S40 | 2453 | 0 | 0 / 2453 | 0.000 |
| CIMS-MN-084-IH-MN-M05688-240618_S30 | 2451 | 0 | 0 / 2451 | 0.000 |
| CIMS-MN-100-IH-MN-M05688-240618_S46 | 2453 | 0 | 0 / 2453 | 0.000 |